BSD Ports

wip/glimmerm 2.5.1 NetBSD

Gene finder developed specifically for eukaryotes

System
NetBSD
Repository
pkgsrc-wip
Maintainer
[email protected]
Categories
wip, biology

Description

A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programing algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations. It uses Interpolated Markov Model(IMM) for selecting the best gene model. The system has been trained for Arabidopsis thaliana, Oryza sativa (rice), and Plasmodium falciparum (the malaria parasite), and should work well on closely related organisms.

Install

From pkgsrc-wip (no binary package):

cd /usr/pkgsrc/wip/glimmerm && make install clean

Dependencies

No port depends on this one.